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You're reading from  R Bioinformatics Cookbook - Second Edition

Product typeBook
Published inOct 2023
PublisherPackt
ISBN-139781837634279
Edition2nd Edition
Concepts
Bioinformatics
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Author (1)
Dan MacLean
Dan MacLean
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Dan MacLean

Professor Dan MacLean has a PhD in molecular biology from the University of Cambridge and gained postdoctoral experience in genomics and bioinformatics at Stanford University in California. Dan is now an honorary professor at the School of Computing Sciences at the University of East Anglia. He has worked in bioinformatics and plant pathogenomics, specializing in R and Bioconductor, and has developed analytical workflows in bioinformatics, genomics, genetics, image analysis, and proteomics at the Sainsbury Laboratory since 2006. Dan has developed and published software packages in R, Ruby, and Python, with over 100,000 downloads combined.
Read more about Dan MacLean

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Getting Gene Ontology information for functional analysis from appropriate databases

The Gene Ontology (GO) is a very useful restricted vocabulary of annotation terms for genes and gene products that describe the biological process, molecular function, or cellular component of an annotated entity. As such, the terms are helpful as data in gene-set enrichment analysis and other functional -omic approaches. In this recipe, we’ll look at how we can prepare a list of gene IDs in a genomic region and get the GO IDs and descriptions for them.

Getting ready

We will just need the biomaRt package from Bioconductor and an internet connection.

How to do it…

Getting GO information can be done using the following steps:

  1. Make connections to Ensembl BioMart and find attributes:
    library(biomaRt)ensembl_connection <- useMart(biomart = "ENSEMBL_MART_ENSEMBL")listDatasets(ensembl_connection)data_set_connection <- useMart("hsapiens_gene_ensembl"...
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R Bioinformatics Cookbook - Second Edition
Published in: Oct 2023Publisher: PacktISBN-13: 9781837634279
© 2023 Packt Publishing Limited All Rights Reserved

Author (1)

author image
Dan MacLean

Professor Dan MacLean has a PhD in molecular biology from the University of Cambridge and gained postdoctoral experience in genomics and bioinformatics at Stanford University in California. Dan is now an honorary professor at the School of Computing Sciences at the University of East Anglia. He has worked in bioinformatics and plant pathogenomics, specializing in R and Bioconductor, and has developed analytical workflows in bioinformatics, genomics, genetics, image analysis, and proteomics at the Sainsbury Laboratory since 2006. Dan has developed and published software packages in R, Ruby, and Python, with over 100,000 downloads combined.
Read more about Dan MacLean

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